def configure_and_run(self):
"""
Configures and runs the application. It will set the exit status of the object in accordance with if any
fatal qc errors were found or not.
:returns: The reports of the application as a dict
"""
try:
config = ConfigFactory.from_config_path(self._config_file)
parser_configurations = config.get("parser_configurations", None)
run_type_recognizer = RunTypeRecognizer(config=config,
runfolder=self._runfolder)
instrument_and_reagent_version = run_type_recognizer.instrument_and_reagent_version(
)
# TODO For now assume symmetric read lengths
both_read_lengths = run_type_recognizer.read_length()
read_length = int(both_read_lengths.split("-")[0])
handler_config = config.get_handler_configs(
instrument_and_reagent_version, read_length)
run_type_summary = RunTypeSummarizer.summarize(
instrument_and_reagent_version, both_read_lengths,
handler_config)
qc_engine = QCEngine(runfolder=self._runfolder,
parser_configurations=parser_configurations,
handler_config=handler_config)
reports = qc_engine.run()
reports["run_summary"] = run_type_summary
self.exit_status = qc_engine.exit_status
return reports
except CheckQCException as e:
log.error(e)
self.exit_status = 1
def configure_and_run(self):
"""
Configures and runs the application. It will set the exit status of the object in accordance with if any
fatal qc errors were found or not.
:returns: The reports of the application as a dict
"""
config = ConfigFactory.from_config_path(self._config_file)
parser_configurations = config.get("parser_configurations", None)
if not Path(self._runfolder).is_dir():
raise RunfolderNotFoundError(
"Could not find runfolder: {}. Are you "
"sure the path is correct?".format(self._runfolder))
run_type_recognizer = RunTypeRecognizer(runfolder=self._runfolder)
instrument_and_reagent_version = run_type_recognizer.instrument_and_reagent_version(
)
# TODO For now assume symmetric read lengths
both_read_lengths = run_type_recognizer.read_length()
read_length = int(both_read_lengths.split("-")[0])
handler_config = config.get_handler_configs(
instrument_and_reagent_version, read_length)
run_type_summary = RunTypeSummarizer.summarize(
instrument_and_reagent_version, both_read_lengths, handler_config)
qc_engine = QCEngine(runfolder=self._runfolder,
parser_configurations=parser_configurations,
handler_config=handler_config)
reports = qc_engine.run()
reports["run_summary"] = run_type_summary
self.exit_status = qc_engine.exit_status
return reports
class TestRunTypeRecognizerFromFolder(TestCase):
def setUp(self):
self.runtype_recognizer = RunTypeRecognizer(runfolder=os.path.join(os.path.dirname(__file__),
"resources", "Rapid"))
def test_instrument_type(self):
expected = "hiseq2500"
actual = self.runtype_recognizer.instrument_type()
self.assertEqual(expected, actual.name())
def test_read_length(self):
expected = "51"
actual = self.runtype_recognizer.read_length()
self.assertEqual(expected, actual)
def test_run_mode(self):
expected = "hiseq2500_rapidrun_v2"
actual = self.runtype_recognizer.instrument_and_reagent_version()
self.assertEqual(expected, actual)
return checkqc_config_dict
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description="Converts CheckQC tresholds to MultiQC conditional format")
parser.add_argument("--runfolder",
type=str,
required=True,
help="Path to runfolder")
parser.add_argument("--config", type=str, help="Path to checkQC config")
args = parser.parse_args()
runfolder = args.runfolder
config = args.config
run_type_recognizer = RunTypeRecognizer(runfolder)
config = ConfigFactory.from_config_path(config)
instrument_and_reagent_version = (
run_type_recognizer.instrument_and_reagent_version())
both_read_lengths = run_type_recognizer.read_length()
read_length = int(both_read_lengths.split("-")[0])
checkqc_config = config.get_handler_configs(instrument_and_reagent_version,
read_length)
checkqc_config_dict = convert_to_dict(checkqc_config)
multiqc_config = convert_to_multiqc_config(checkqc_config_dict)
with open("qc_thresholds.yaml", "w") as outfile:
yaml.dump(multiqc_config, outfile)
def _create_runtype_recognizer(self, instrument_name):
with mock.patch.object(RunfolderReader, 'read_run_info_xml',
return_value={"RunInfo": {"Run": {"Instrument": instrument_name}}}), \
mock.patch.object(RunfolderReader, 'read_run_parameters_xml', return_value=None):
return RunTypeRecognizer(runfolder='foo')
def setUp(self):
self.runtype_recognizer = RunTypeRecognizer(runfolder=os.path.join(os.path.dirname(__file__),
"resources", "Rapid"))